An important technique currently used in bioanalysis and in the emerging field of genomics is the polymerase chain reaction (PCR) amplification of DNA. As a result of this powerful tool, it is possible to start with otherwise undetectable amounts of DNA and create ample amounts of the material for subsequent analysis. PCR uses a repetitive series of steps to create copies of polynucleotide sequences located between two initiating (“primer”) sequences. Starting with a template, two primer sequences (usually about 15-30 nucleotides in length), PCR buffer, free deoxynucleoside tri-phosphates (dNTPs), and thermostable DNA polymerase (commonly TAQ polymerase from Thermus aquaticus), these components are mixed, and heated to separate the double-stranded DNA. A subsequent cooling step allows the primers to anneal to complementary sequences on single-stranded DNA molecules containing the sequence to be amplified. Replication of the target sequence is accomplished by the DNA polymerase, which produces a strand of DNA that is complementary to the template. Repetition of this process doubles the number of copies of the sequence of interest, and multiple cycles increase the number of copies exponentially.
Since PCR requires repeated cycling between higher and lower temperatures, PCR devices must be fabricated from materials capable of withstanding such temperature changes. The materials must be mechanically and chemically stable at high temperatures, and capable of withstanding repeated temperature changes without mechanical degradation. Furthermore, the materials must be compatible with the PCR reaction itself, and not inhibit the polymerase or bind DNA.
Conventional PCR is typically carried out in tubes, microplates, and capillaries, all of which could be sealed conveniently. However, the geometry of these tubes, microplates, and capillaries render them not suitable for evanescent wave detection methods.